I read document of wxpython-phoenix and found that state of toolbar items should be changed by wx.ToolBar.EnableTool(). Rewriting app/builder/builder.py to use wx.ToolBar.EnableTool(), Builder experiment seems to terminate correctly (Exactly to say, the problem was not termination of experiment but updating satatus of Run/Stop buttons). I created feature-wx4 branch in my repository and pushed this fix.
Regarding the issue of EXEC_HOHIDE flag, wx.EXEC_HIDE_CONSOLE didn’t work in my environment. Instead, wx.EXEC_SHOW_CONSOLE works fine. I’d appreciate if you could test wx.EXEC_SHOW_CONSOLE in your environment.